|
| Status |
Public on Nov 23, 2017 |
| Title |
L1600253_NS224_fragmented_extracellular |
| Sample type |
SRA |
| |
|
| Source name |
Extracellular parasites
|
| Organism |
Toxoplasma gondii |
| Characteristics |
group: Extracellular parasites
replicate: Replicate 2
|
| Treatment protocol |
Prior to havesting, the parasite cultures were treated for about 10min with cyclohexamide (100ug/ml).
|
| Growth protocol |
Type I Toxoplasma gondii was grown on human foreskin fibroblasts and intracellular or extracellular parasites collected after 24 hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Aftter collection, the parasite samples were divided into two samples: one sample was used for ribosome profling, as previously described (Ingolia et al, 2009) and the other sample was used for high throughput RNA-sequencing.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-seq
|
| Data processing |
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to GT whole genome (V29) using the STAR aligner with default parameters
Supplementary_files_format_and_content: Read couts were obtained using HTSeq
|
| |
|
| Submission date |
May 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Musa Hassan |
| Organization name |
University of Edinburgh
|
| Department |
Roslin
|
| Lab |
Hassan
|
| Street address |
Easter Bush
|
| City |
Edinburgh |
| State/province |
Scotland |
| ZIP/Postal code |
EH25 9RG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16774 |
| Series (1) |
| GSE99395 |
Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii |
|
| Relations |
| BioSample |
SAMN07175851 |
| SRA |
SRX2867499 |
